User: Rory Stark

gravatar for Rory Stark
Rory Stark1.8k
Reputation:
1,830
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Location:
CRUK, Cambridge, UK
Last seen:
1 week, 5 days ago
Joined:
4 years, 6 months ago
Email:
r*********@cruk.cam.ac.uk

I am Principal Bioinformatics Analyst at the University of Cambridge, leading the Analysis Team in the Bioinformatics Core at Cancer Research UK's Cambridge Institute.

Posts by Rory Stark

<prev • 340 results • page 1 of 34 • next >
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Answer: A: How to set the parameter "fragmentSize" in DiffBind and set parameter for paired
... I agree with Gord's answer, but wanted to elaborate a bit. The difference is most likely the normalization step. edgeR uses the TMM method which relies on a core of sites that don't systematically change their binding affinities. While this assumption of usually true for RNA-seq, there are many ChI ...
written 17 days ago by Rory Stark1.8k
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Answer: A: How to set the parameter "fragmentSize" in DiffBind and set parameter for paired
... For the fragment sizes, you are not setting the dba.read()parameter correctly. You should never set a value for config as a parameter. You want to either set the parameter value directly: > myDBA <- dba.read(myDBA,fragmentSize=c(chip_1 , chip_2 , input_1 , input_2)) or set this as the defa ...
written 18 days ago by Rory Stark1.8k
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Answer: A: Diffbind heatmap color change
... Hi Andrew- The heatmap plotting code changed a while back. Try setting colScheme="Blues". This will set the color scheme using RColorBrewer: col = colorRampPalette(brewer.pal(9,"Blues"))(256) You can also set colScheme to any vector of colors, which will be used for the heatmap as if you passed ...
written 20 days ago by Rory Stark1.8k
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Answer: A: how overlap between peaks is calculated in diffbind
... Hello Aimin- I tracked this down to a bug in DiffBind that arises when a) dba.peakset() is used to add a specific set of peaks (rather than just the sample sheet being loaded in dba()) and b) the added peakset is not sorted. I have already checked in a fix that will appear as DiffBind 2.4.8 in the ...
written 5 weeks ago by Rory Stark1.8k
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Answer: A: PCR bottleneck coefficient (PBC)
... No, ChIPQC does not compute these metrics. It does compute FRiP (fraction of reads in peaks) and duplication rate (fraction of reads that map to the same location as another read).. -Rory ...
written 5 weeks ago by Rory Stark1.8k
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Answer: A: Question: DiffBind dba.report() output: the output when setting bCounts=TRUE
... In the default case, where bNormalised=TRUE, the values are the normalised read counts that are used by the analysis package. If, in the call to dba.analyze(), bSubControl=TRUE (default), the number of reads in the control are subtracted first, with a minimum read count of 1 before normalisation. I ...
written 5 weeks ago by Rory Stark1.8k
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Answer: A: Diffbind - "dba.report" showing values with less significant figures?
... Hi Wes- Yes indeed, a change was made to limit the number of significant digits for the main stats in the report. This was done for two reasons: Reporting 8+ significant digits is inherently misleading. While the computer is perfectly happy to calculate these digits, it gives a false sense of pr ...
written 5 weeks ago by Rory Stark1.8k
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Comment: C: Diffbind: retrieve raw peaks per sample
... I'm not sure I understand your code -- what is the call to peaks() on the third line? -R ...
written 5 weeks ago by Rory Stark1.8k
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Comment: C: Technical details of DiffBind correlation analysis
... In an occupancy analysis, the score is as described in my original answer (normalised peak score as specified in the peak file). The calculation of the original scores depends on the peak caller. For example, the default score for MACS peaks is -log10(p-value) (peak confidence). You can change it to ...
written 5 weeks ago by Rory Stark1.8k
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Comment: C: DiffBind : More fragment sizes than libraries
... I've checked in a change so that if you set initString=NULL, it will not add the "_", so you can specify a full filepath in the "file" parameter. ...
written 8 weeks ago by Rory Stark1.8k

Latest awards to Rory Stark

Scholar 9 weeks ago, created an answer that has been accepted. For A: DiffBind "no lines available in input" error
Guru 3 months ago, received more than 100 upvotes.
Popular Question 3 months ago, created a question with more than 1,000 views. For a diffBind problem
Scholar 3 months ago, created an answer that has been accepted. For A: DiffBind "no lines available in input" error
Popular Question 4 months ago, created a question with more than 1,000 views. For a diffBind problem
Scholar 6 months ago, created an answer that has been accepted. For A: DiffBind "no lines available in input" error
Scholar 6 months ago, created an answer that has been accepted. For A: DiffBind "no lines available in input" error
Autobiographer 11 months ago, has more than 80 characters in the information field of the user's profile.
Scholar 16 months ago, created an answer that has been accepted. For A: DiffBind "no lines available in input" error
Scholar 16 months ago, created an answer that has been accepted. For A: What does dba.PCA in DiffBind exactly do?
Scholar 16 months ago, created an answer that has been accepted. For A: DiffBind matrix of values
Scholar 16 months ago, created an answer that has been accepted. For A: ChIPQC and/or Diffbind - retrieving normalized read counts for peaks from single
Teacher 17 months ago, created an answer with at least 3 up-votes. For A: Work with GRanges objects in DiffBind
Scholar 18 months ago, created an answer that has been accepted. For A: What does dba.PCA in DiffBind exactly do?
Scholar 20 months ago, created an answer that has been accepted. For A: What does dba.PCA in DiffBind exactly do?
Scholar 21 months ago, created an answer that has been accepted. For A: What does dba.PCA in DiffBind exactly do?
Scholar 22 months ago, created an answer that has been accepted. For A: Work with GRanges objects in DiffBind
Teacher 22 months ago, created an answer with at least 3 up-votes. For A: diffBind correlation plot
Teacher 22 months ago, created an answer with at least 3 up-votes. For A: Work with GRanges objects in DiffBind
Scholar 22 months ago, created an answer that has been accepted. For A: diffBind correlation plot
Scholar 22 months ago, created an answer that has been accepted. For A: Clarification about the functionality of dba.count and dba.analyze
Scholar 22 months ago, created an answer that has been accepted. For A: subset of samples from dba object in DiffBind
Scholar 2.1 years ago, created an answer that has been accepted. For A: problem with characters in chromosome names in DiffBind dba
Teacher 2.1 years ago, created an answer with at least 3 up-votes. For A: diffBind correlation plot
Scholar 2.2 years ago, created an answer that has been accepted. For A: diffBind correlation plot

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